HI All,
I need to translate the multi fasta file nucleotide sequences to aminoacid into 6 reading frames and select the best reading frame that defines the nucleotide sequences. Do any one of you have any perl script or any tool that can do this will be a great help.
Regards
Emboss has sixpack to do that: http://emboss.sourceforge.net/apps/cvs/emboss/apps/sixpack.html
Here is the corrected code from shane.neely, which is otherwise very elegant and useful:
beans = "TGACTGTGTTTCTGAACAATAAATGACTTAAACCAGGTATGGCTGCCGATGGTTATCTT"
gencode = {
'ATA':'I', 'ATC':'I', 'ATT':'I', 'ATG':'M',
'ACA':'T', 'ACC':'T', 'ACG':'T', 'ACT':'T',
'AAC':'N', 'AAT':'N', 'AAA':'K', 'AAG':'K',
'AGC':'S', 'AGT':'S', 'AGA':'R', 'AGG':'R',
'CTA':'L', 'CTC':'L', 'CTG':'L', 'CTT':'L',
'CCA':'P', 'CCC':'P', 'CCG':'P', 'CCT':'P',
'CAC':'H', 'CAT':'H', 'CAA':'Q', 'CAG':'Q',
'CGA':'R', 'CGC':'R', 'CGG':'R', 'CGT':'R',
'GTA':'V', 'GTC':'V', 'GTG':'V', 'GTT':'V',
'GCA':'A', 'GCC':'A', 'GCG':'A', 'GCT':'A',
'GAC':'D', 'GAT':'D', 'GAA':'E', 'GAG':'E',
'GGA':'G', 'GGC':'G', 'GGG':'G', 'GGT':'G',
'TCA':'S', 'TCC':'S', 'TCG':'S', 'TCT':'S',
'TTC':'F', 'TTT':'F', 'TTA':'L', 'TTG':'L',
'TAC':'Y', 'TAT':'Y', 'TAA':'_', 'TAG':'_',
'TGC':'C', 'TGT':'C', 'TGA':'_', 'TGG':'W'}
basepairs = {'A':'T', 'C':'G', 'G':'C', 'T':'A'}
def translate_frameshifted( sequence ):
translate = ''.join([gencode.get(sequence[3*i:3*i+3],'X') for I in range(len(sequence)//3)])
return translate
def reverse_complement( sequence ):
reversed_sequence = (sequence[::-1])
rc = ''.join([basepairs.get(reversed_sequence[i], 'X') for I in range(len(sequence))])
return rc
print(translate_frameshifted(beans[0:])) # first frame
print(translate_frameshifted(beans[1:])) # second frame
print(translate_frameshifted(beans[2:])) # third frame
print(translate_frameshifted(reverse_complement(beans))) # negative first frame
print(translate_frameshifted(reverse_complement(beans[:len(beans)-1]))) # negative second frame
print(translate_frameshifted(reverse_complement(beans[:len(beans)-2]))) # negative third frame
# This ::-1 syntax in python means reverse the string.
You may use UGENE Workflow Designer. No scripts needed, only GUI manipulations 1) Download UGENE http://ugene.unipro.ru/ 2) Open Workflow Designer from the Tools menu 3) Create a scheme with the following elements: "Read Sequence" -> "Amino Translation" -> "Write sequence".
Try use the orfpredictor - it gives you the best and all 6-frames, and also retrieve the cds.
I have written a program in Python 3 that takes a nucleotide FASTA file as input, and translates each sequence in that file in the frame which produces the fewest number of stop codons.
The software transcribes each sequence in all six frames and counts the number of STOP codons in each. It then writes the original sequence in the 'optimal' frame to an output FASTA file, with the frame name appended to the contig name. In cases where there are multiple optimal frames Optimal Translate writes both into the output FASTA file. It only needs Python 3 to run and works on both DNA and RNA sequences.
The software can be run in Python or as a Geneious 11 plugin on Windows.
You can access it here: https://github.com/Kzra/Optimal-Translate
Try this python script from this resource, I haven't tested it though.
[translatedna.py]read a fasta file, do 6-frame translation, print best protein seqs as fasta
beware, "haven't tested" is a big risk in the case there is in fact a mistake or bug. In general, for routine tasks like this, in my opinion no new code should be written at all given the presence of highly stable and well tested code. The reason why I like to stress this is that you can taint all your downstream analysis, by e.g. a typo in the genetic code matrix.
Here is some python to translate all six frames of DNA.
beans = "TGACTGTGTTTCTGAACAATAAATGACTTAAACCAGGTATGGCTGCCGATGGTTATCTT"
gencode = {
'ATA':'I', 'ATC':'I', 'ATT':'I', 'ATG':'M',
'ACA':'T', 'ACC':'T', 'ACG':'T', 'ACT':'T',
'AAC':'N', 'AAT':'N', 'AAA':'K', 'AAG':'K',
'AGC':'S', 'AGT':'S', 'AGA':'R', 'AGG':'R',
'CTA':'L', 'CTC':'L', 'CTG':'L', 'CTT':'L',
'CCA':'P', 'CCC':'P', 'CCG':'P', 'CCT':'P',
'CAC':'H', 'CAT':'H', 'CAA':'Q', 'CAG':'Q',
'CGA':'R', 'CGC':'R', 'CGG':'R', 'CGT':'R',
'GTA':'V', 'GTC':'V', 'GTG':'V', 'GTT':'V',
'GCA':'A', 'GCC':'A', 'GCG':'A', 'GCT':'A',
'GAC':'D', 'GAT':'D', 'GAA':'E', 'GAG':'E',
'GGA':'G', 'GGC':'G', 'GGG':'G', 'GGT':'G',
'TCA':'S', 'TCC':'S', 'TCG':'S', 'TCT':'S',
'TTC':'F', 'TTT':'F', 'TTA':'L', 'TTG':'L',
'TAC':'Y', 'TAT':'Y', 'TAA':'_', 'TAG':'_',
'TGC':'C', 'TGT':'C', 'TGA':'_', 'TGG':'W'}
def translate_frameshifted( sequence ):
translate = ''.join([gencode.get(sequence[3*i:3*i+3],'X') for i in range(len(sequence)//3)])
return translate
print translate_frameshifted(beans[0:]) # first frame
print translate_frameshifted(beans[1:]) # second frame
print translate_frameshifted(beans[2:]) # third frame
print translate_frameshifted(beans[::-1][0:]) # first frame from end
print translate_frameshifted(beans[::-1][1:]) # second frame from end
print translate_frameshifted(beans[::-1][2:]) # third frame from end
# This ::-1 syntax in python means reverse the string.
Result:
_LCF_TINDLNQVWLPMVI
DCVSEQ_MT_TRYGCRWLS
TVFLNNK_LKPGMAADGYL
FYW_PSVWTKFSK_QVFVS
SIGSRRYGPNSVNNKSLCQ
LLVAVGMDQIQ_ITSLCVS
Result:
_LCF_TINDLNQVWLPMVI
DCVSEQ_MT_TRYGCRWLS
TVFLNNK_LKPGMAADGYL
KITIGSHTWFKSFIVQKHS
R_PSAAIPGLSHLLFRNTV
DNHRQPYLV_VIYCSETQS
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version 2.3.6
Hello, the Emboss util doesn't work:
Even though a minimum size for ORFs is set, smaller ORFs are reported, and the first AA is not always M, but it should be.